PDBsum entry 2kem

Hydrolase

PDB id: 2kem

Contents

Protein chain

194 a.a. *

Metals

_ZN

* Residue conservation analysis

PDB id:

2kem

Name:

Hydrolase

Title:

Extended structure of citidine deaminase domain of apobec3g

Structure:

DNA dc->du-editing enzyme apobec-3g. Chain: a. Fragment: unp residues 191-284. Synonym: apobec-related cytidine deaminase, arcd, apobec-related protein, arp-9, cem-15, cem15. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: apobec3g. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

10 models

Authors:

E.Harjes,P.J.Gross,K.Chen,Y.Lu,K.Shindo,R.Nowarski,J.D.Gross, M.Kotler,R.S.Harris,H.Matsuo

Key ref:

E.Harjes et al. (2009). An extended structure of the APOBEC3G catalytic domain suggests a unique holoenzyme model. J Mol Biol, 389, 819-832. PubMed id: 19389408 DOI: 10.1016/j.jmb.2009.04.031

Date:

30-Jan-09 Release date: 02-Jun-09

Protein chain

Q9HC16  (ABC3G_HUMAN) -  DNA dC->dU-editing enzyme APOBEC-3G from Homo sapiens

Seq: 384 a.a.

Struc: 194 a.a.*

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.5.4.38 - single-stranded Dna cytosine deaminase.
• Reaction: a 2'-deoxycytidine in single-stranded DNA + H2O + H⁺ = a 2'-deoxyuridine in single-stranded DNA + NH4⁺

DOI no: 10.1016/j.jmb.2009.04.031

J Mol Biol 389:819-832 (2009)

PubMed id: 19389408

An extended structure of the APOBEC3G catalytic domain suggests a unique holoenzyme model.

E.Harjes, P.J.Gross, K.M.Chen, Y.Lu, K.Shindo, R.Nowarski, J.D.Gross, M.Kotler, R.S.Harris, H.Matsuo.

ABSTRACT

Human APOBEC3G (A3G) belongs to a family of polynucleotide cytidine deaminases. This family includes APOBEC1 and AID, which edit APOB mRNA and antibody gene DNA, respectively. A3G deaminates cytidines to uridines in single-strand DNA and inhibits the replication of human immunodeficiency virus-1, other retroviruses, and retrotransposons. Although the mechanism of A3G-catalyzed DNA deamination has been investigated genetically and biochemically, atomic details are just starting to emerge. Here, we compare the DNA cytidine deaminase activities and NMR structures of two A3G catalytic domain constructs. The longer A3G191-384 protein is considerably more active than the shorter A3G198-384 variant. The longer structure has an alpha1-helix (residues 201-206) that was not apparent in the shorter protein, and it contributes to catalytic activity through interactions with hydrophobic core structures (beta1, beta3, alpha5, and alpha6). Both A3G catalytic domain solution structures have a discontinuous beta2 region that is clearly different from the continuous beta2 strand of another family member, APOBEC2. In addition, the longer A3G191-384 structure revealed part of the N-terminal pseudo-catalytic domain, including the interdomain linker and some of the last alpha-helix. These structured residues (residues 191-196) enabled a novel full-length A3G model by providing physical overlap between the N-terminal pseudo-catalytic domain and the new C-terminal catalytic domain structure. Contrary to predictions, this structurally constrained model suggested that the two domains are tethered by structured residues and that the N- and C-terminal beta2 regions are too distant from each other to participate in this interaction.

Selected figure(s)

Figure 4.
Fig. 4. A structural comparison A3G191-384-2K3A (PDB ID code 2kem; this study), A3G193-384 (PDB ID code 2kbo^20), A3G197-380 (PDB ID code 3e1u^22), and A2 (PDB ID code 2nyt^23). (a–d) α-carbon-traced ribbon schematics for the aforementioned structures. The β2 regions are highlighted by blue ovals and shown in green in (b)–(d). The interdomain linker region in (a) is indicated by an arrow. (e–h) Polypeptide backbone and chemical contact schematics for the β2 and β1 regions of A3G191-384-2K3A, A3G193-384, A3G197-380, and A2, respectively. Amino acid positions are numbered and, if the residue is conserved, shown in red. In (e) and (f), observed NOEs are indicated by arrows. In (g) and (h), predicted hydrogen bonds are indicated by broken lines, and labels correspond to distances between the amide nitrogen and the carbonyl oxygen atoms.

Figure 7.
Fig. 7. HIV restriction activity of A3G-2K3A. (a) A histogram reporting the infectivity of Vif-deficient HIV-1 produced in the presence of a GFP control expression vector, wild-type A3G-GFP, or full-length A3G-2K3A-GFP. (b) Representative immunoblots of virus particles and cellular lysates A3G, CA and Tubulin were detected using anti-GFP, anti-p24 and anti-tubulin antibodies, respectively.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2009, 389, 819-832) copyright 2009.

Figures were selected by an automated process.